Programmatic Access To Biological Databases (Perl). 1 October 2012

1. Web services game

2. Hypothetical scenario to understand
REST and SOAP Web Services
A biologist wants a software application to visualize chromosome sequences
A. The biologist ask a programmer
B. The programmer creates an application
C. The biologist uses the application
A. The programmer creates an application
1. The programmer finds a web service providing genome sequences
2. The programmer looks for documentation about how to request sequences in this service
3. Programmer encodes logic to retrieve and present information into an application
B. The biologist uses the application
1. The biologist queries the application
2. The application sends a request to the service
3. The service provides a response to the application
4. The application present the information to the biologist

3. Web Services
How should I invoke you?
Documentation
Make a request
Results
Web server
Application
describes the methods and variables to query the service
1
2
3
4
2
Developer

4. REST Web Services
How should I invoke you?
Documentation
Make a request ( GET or POST)
Results (data + status)
Web server
Sometimes a WADL file is available in the server to describe
the service
1
2
3
4
2
WADLor
Informal
Description
Formal
Description
Application
Developer

5. SOAP Web Services
How should I invoke you?
Documentation (WSDL)
Make a SOAP request
Web server1
2
3
WSDL
Method / Parameters Data
4
3 4SOAP request SOAP response
and
Informal
Description
Formal
Description
Results (SOAP response)
Application
Developer

6. Biologist
Application

7. Programmer
Application

8. Personal computer
Application

9. Application
REST
Application

10. Application
SOAP
Application

11. Server

12. Web service
REST

13. Web service
SOAP

14. Internet

15. Request: documentation
Please send me
documentation
about how to
query the service
using REST

16. Request: documentation
Please send me
documentation
about how to
query the service
using SOAP

17. Response: documentation
GET
http://{domain}/{service}?gene={geneID}&specie={specieID}
Domain
• www.abc.org
Services
• sequence
• annotations
Methods
• gene
• specie
REST
Informal description
WADL
www.abc.org/ws.wadl

18. Response: documentation
<application>
<resources base="http://www.abc.org">
<resource path="/sequence">
<method>
<request>
<param name="gene" type="xs:string"/>
<param name="specie" type="xs:string"/>
</request>
<response>
<representation mediaType="text/plain"/>
</response>
<method>
</resource>
<resource path="/annotation">
<method>
<request>
<param name="gene" type="xs:string"/>
<param name="specie" type="xs:string"/>
</request>
<response>
<representation mediaType="text/plain"/>
</response>
<method>
</resource>
</resources>
</application>
WADL
REST
Formal description
http://www.abc.org/ws.wadl

19. Response: documentation
SOAP
Informal description
WSDL
www.abc.org/ws.wsdl
Domain
• www.abc.org
Services
• sequence
• annotations
Methods
• gene
• specie

20. Response: documentation
<wsdl:definitions name="abcService">
<wsdl:types>
<xs:complexType name="getSequence">
<xs:sequence>
<xs:element name="sequence" type="xs:string"/>
<xs:element name="infoRequest" type="requestInfo"/>
</xs:sequence>
</xs:complexType>
</xs:complexType>
<xs:complexType name="getAnnotations">
<xs:sequence>
<xs:element name="annotations" type="xs:string"/>
<xs:element name="infoRequest" type="requestInfo"/>
</xs:sequence>
</xs:complexType>
</xs:complexType>
<xs:complexType name="resultInfo">
<xs:sequence>
<xs:element name="gene" type="xs:string"/>
<xs:element name="specie" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</wsdl:types>
<wsdl:message name="getSequence">
<wsdl:part element="getSequence" name="parameters" />
</wsdl:message>
<wsdl:message name="getAnnotations">
<wsdl:part element="getAnnotations" name="parameters" />
</wsdl:message>
<wsdl:portType name="abcService">
<wsdl:operation name="getSequence">
<wsdl:input message="getSequence" name="getSequence" />
<wsdl:output message="getSequenceResponse" name="getSequenceResponse" />
</wsdl:operation>
<wsdl:operation name="getAnnotations">
<wsdl:input message="getAnnotations" name="getAnnotations" />
<wsdl:output message="getAnnotationsResponse" name="getAnnotationsResponse" />
</wsdl:operation>
</wsdl:portType>
<wsdl:binding name="abcServiceSoapBinding" type="abcService">
<wsdl:operation name="getSequence">
<soap:operation soapAction="getSequence" style="document"/>
<wsdl:input name="getSequence">
<soap:body use="literal"/>
</wsdl:input>
<wsdl:output name="getSequenceResponse">
<soap:body use="literal"/>
</wsdl:output>
<wsdl:fault name="abcServiceException">
<soap:fault name="abcServiceException" use="literal"/>
</wsdl:fault>
</wsdl:operation>
<wsdl:operation name="getAnnotations">
<soap:operation soapAction="getAnnotations" style="document"/>
<wsdl:input name="getAnnotations">
<soap:body use="literal"/>
</wsdl:input>
<wsdl:output name="getAnnotationsResponse">
<soap:body use="literal"/>
</wsdl:output>
<wsdl:fault name="abcServiceException">
<soap:fault name="abcServiceException" use="literal"/>
</wsdl:fault>
</wsdl:operation>
</wsdl:binding>
<wsdl:service name="abcService">
<wsdl:port binding="abcServiceSoapBinding" name="abcServicePort">
<soap:address location="http://abc.org"/>
</wsdl:port>
</wsdl:service>
</wsdl:definitions>
SOAP
WSDL
Formal description
http://www.abc.org/ws.wsdl

21. REST request
http://abc.org/sequence?gene=BRCA1&specie=human
URL
Application

22. SOAP request
<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/">
<soapenv:Header/>
<soapenv:Body>
<getSequence>
<infoRequest>
<gene>BRCA1</gene>
<specie>human</specie>
</infoRequest>
</getSequence>
</soapenv:Body>
</soapenv:Envelope>
SOAP envelope
Application

23. Status:
200
Response:
ATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGATT
TAGGACCAATAAGTCTTAATTGGTTTGAAGAACTTTCTTCAGAAGCTCCACCCTATAATTCTGAACCTGC
AGAAGAATCTGAACATAAAAACAACAATTACGAACCAAACCTATTTAAAACTCCACAAAGGAAACCATCT
TATAATCAGCTGGCTTCAACTCCAATAATATTCAAAGAGCAAGGGCTGACTCTGCCGCTGTACCAATCTC
CTGTAAAAGAATTAGATAAATTCAAATTAGACTTAGGAAGGAATGTTCCCAATAGTAGACATAAAAG...
REST response

24. <soap:Envelope xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/">
<soap:Body>
<getSequenceResponse>
<sequenceResponse>
<resultSet/>
<resultInfo>
<gene>BRCA1</gene>
<specie>human</specie>
<seqeunceResults>
ATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGATT
TAGGACCAATAAGTCTTAATTGGTTTGAAGAACTTTCTTCAGAAGCTCCACCCTATAATTCTGAACCTGC
AGAAGAATCTGAACATAAAAACAACAATTACGAACCAAACCTATTTAAAACTCCACAAAGGAAACCATCT
TATAATCAGCTGGCTTCAACTCCAATAATATTCAAAGAGCAAGGGCTGACTCTGCCGCTGTACCAATCTC
CTGTAAAAGAATTAGATAAATTCAAATTAGACTTAGGAAGGAATGTTCCCAATAGTAGACATAAAAG...
</sequenceResults>
</resultInfo>
</sequenceResponse>
</getSequenceResponse>
</soap:Body>
</soap:Envelope>
SOAP response

25. Application response
BRCA1 Human
ATGCCTATTGGATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGATT
TAGGACCAATAAGTCTTAATTGGTTTGAAGAACTTTCTTCAGAAGCTCCACCCTATAATTCTGAACCTGC
AGAAGAATCTGAACATAAAAACAACAATTACGAACCAAACCTATTTAAAACTCCACAAAGGAAACCATCT
TATAATCAGCTGGCTTCAACTCCAATAATATTCAAAGAGCAAGGGCTGACTCTGCCGCTGTACCAATCTC
CTGTAAAAGAATTAGATAAATTCAAATTAGACTTAGGAAGGAATGTTCCCAATAGTAGACATAAAAG...
Application

26. Thank you!
13/12/2018
26
ProteomicsServicesTeam